Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 29
Found at i:3115822 original size:55 final size:55
Alignment explanation
Indices: 3115754--3116068 Score: 362
Period size: 55 Copynumber: 5.7 Consensus size: 55
3115744 GTTTTTTAAC
*
3115754 TAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAAT
1 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAAGAAAT
* * * * * *
3115809 TAATTCTAATTTTCAAAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAAT
1 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAAGAAAT
*
3115864 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAAGAAAC
1 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAAGAAAT
* * * * *
3115919 TAAGTTTGATTTTCAGAAGTTTGTTGACGATTTTCAAATTAGTTTTTAAAGAAAC
1 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAAGAAAT
* * * * * * * * *
3115974 TAAGTCTGATTTTAAAAACTTTCTTGATGATTTTTAAAAGAACTTTCAAACAAAT
1 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAAGAAAT
* * * ** * *
3116029 TAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTAAAATGA
1 TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGA
3116069 ATTTGAAAAA
Statistics
Matches: 219, Mismatches: 41, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
54 9 0.04
55 210 0.96
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (55 bp):
TAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAAGAAAT
Found at i:3116023 original size:165 final size:164
Alignment explanation
Indices: 3115751--3116068 Score: 447
Period size: 165 Copynumber: 1.9 Consensus size: 164
3115741 TGTGTTTTTT
* *
3115751 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAATTAATTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAACTAAGTCT
* * * * * * *
3115816 AATTTTCAAAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAATTAAGTCTGATTTTCAGA
66 AATTTTAAAAACTTTCTTGATGATTTTTAAAAGAACTTTCAAACAAATTAAGCCTAATTTTCAGA
*
3115881 AGTTTCTTGACGATTTTCAAATGAGCTTTTAAAGA
131 AGTTTCTTGACG-TTTTAAAATGAGCTTTTAAAGA
* * * * *
3115916 AACTAAGTTTGATTTTCAGAAGTTTGTTGACGATTTTCAAATTAGTTTTTAAAGAAACTAAGTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAACTAAGTCT
* * *
3115981 GATTTTAAAAACTTTCTTGATGATTTTTAAAAGAACTTTCAAACAAATTAAGCCTAATTTTTAGG
66 AATTTTAAAAACTTTCTTGATGATTTTTAAAAGAACTTTCAAACAAATTAAGCCTAATTTTCAGA
* *
3116046 GGTTTCTTGATGTTTTAAAATGA
131 AGTTTCTTGACGTTTTAAAATGA
3116069 ATTTGAAAAA
Statistics
Matches: 133, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
164 10 0.08
165 123 0.92
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (164 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAACTAAGTCT
AATTTTAAAAACTTTCTTGATGATTTTTAAAAGAACTTTCAAACAAATTAAGCCTAATTTTCAGA
AGTTTCTTGACGTTTTAAAATGAGCTTTTAAAGA
Found at i:3116459 original size:73 final size:73
Alignment explanation
Indices: 3116349--3116586 Score: 291
Period size: 73 Copynumber: 3.2 Consensus size: 73
3116339 CTTGAGAGAT
* * * * * *
3116349 CTTCGTCTCGCTTGAGATAGTTTTACTCGAAACAAAATTTTATTTCACTCGAGATTGTTTTTCTT
1 CTTCGTCTCACTTGAGACAATTTTACTCGAAAAAAAATTTTATATCACTTGAGATTGTTTTTCTT
3116414 AAAACAAA
66 AAAACAAA
* * * * *
3116422 CTTCGTCTCACTTTAGACAATTTCACTCGAAATAAAATTTTATCTCACTTGAGATTATTTTTCTT
1 CTTCGTCTCACTTGAGACAATTTTACTCGAAAAAAAATTTTATATCACTTGAGATTGTTTTTCTT
3116487 AAAACAAA
66 AAAACAAA
* *
3116495 CTTCGTCTCGCTTGAGACAATTTTTTACTCAAAACAAGAAATTTTATATCACTTG-GATTG-TTT
1 CTTCGTCTCACTTGAGACAA--TTTTACTCGAAA-AA-AAATTTTATATCACTTGAGATTGTTTT
3116558 TCTTAAAACAAA
62 TCTTAAAACAAA
* *
3116570 TTTCATCTCACTTGAGA
1 CTTCGTCTCACTTGAGA
3116587 AAGTTTCCCC
Statistics
Matches: 142, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
73 82 0.58
75 39 0.27
76 5 0.04
77 16 0.11
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (73 bp):
CTTCGTCTCACTTGAGACAATTTTACTCGAAAAAAAATTTTATATCACTTGAGATTGTTTTTCTT
AAAACAAA
Found at i:3116509 original size:36 final size:36
Alignment explanation
Indices: 3116393--3116586 Score: 106
Period size: 37 Copynumber: 5.3 Consensus size: 36
3116383 AAATTTTATT
* *
3116393 TCACTCGAGATTGTTTTTCTTAAAACAAACTTCGTC
1 TCACTTGAGATTATTTTTCTTAAAACAAACTTCGTC
* ** ** * * **
3116429 TCACTTTAGACAATTTCACTCGAAATA-AAATTTTATC
1 TCACTTGAGATTATTTTTCT-TAAA-ACAAACTTCGTC
3116466 TCACTTGAGATTATTTTTCTTAAAACAAACTTCGTC
1 TCACTTGAGATTATTTTTCTTAAAACAAACTTCGTC
* ** * * ** *
3116502 TCGCTTGAGACAATTTTTTACTCAAAACAAGAAATTTTATA
1 TCACTTGAGATTA-TTTTT-CTTAAAAC---AAACTTCGTC
* * *
3116543 TCACTTG-GATT-GTTTTCTTAAAACAAATTTCATC
1 TCACTTGAGATTATTTTTCTTAAAACAAACTTCGTC
3116577 TCACTTGAGA
1 TCACTTGAGA
3116587 AAGTTTCCCC
Statistics
Matches: 114, Mismatches: 35, Indels: 19
0.68 0.21 0.11
Matches are distributed among these distances:
34 15 0.13
35 3 0.03
36 33 0.29
37 37 0.32
38 12 0.11
40 2 0.02
41 12 0.11
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (36 bp):
TCACTTGAGATTATTTTTCTTAAAACAAACTTCGTC
Found at i:3116581 original size:34 final size:34
Alignment explanation
Indices: 3116456--3116586 Score: 102
Period size: 34 Copynumber: 3.6 Consensus size: 34
3116446 ACTCGAAATA
*
3116456 AAATTTTATCTCACTTGAGATTATTTTTCTTAAAAC
1 AAATTTCATCTCACTTGAGA-T-TTTTTCTTAAAAC
* * * *
3116492 AAACTTCGTCTCGCTTGAGACAATTTTTTACTCAAAAC
1 AAATTTCATCTCACTTGAG---ATTTTTT-CTTAAAAC
* *
3116530 AAGAAATTTTATATCACTTG-GATTGTTTTCTTAAAAC
1 ---AAATTTCATCTCACTTGAGATT-TTTTCTTAAAAC
3116567 AAATTTCATCTCACTTGAGA
1 AAATTTCATCTCACTTGAGA
3116587 AAGTTTCCCC
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
34 15 0.21
35 2 0.03
36 15 0.21
37 15 0.21
38 12 0.16
39 1 0.01
40 1 0.01
41 12 0.16
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (34 bp):
AAATTTCATCTCACTTGAGATTTTTTCTTAAAAC
Found at i:3117262 original size:139 final size:139
Alignment explanation
Indices: 3117012--3117660 Score: 1091
Period size: 139 Copynumber: 4.7 Consensus size: 139
3117002 GGTAAATTAG
*
3117012 TCAACATTTCCAGTGGAGAGTTCATAATGATAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
*
3117077 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACACATGGAGTTGAATCAGCAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
3117142 CTCGAGGGA
131 CTCGAGGGA
* *
3117151 TCAACATTTTCAGTGGATAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
*
3117216 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATTAGCAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
*
3117281 CTTGAGGGA
131 CTCGAGGGA
* * *
3117290 TCAACATTTCCAGTTGAGAGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * * *
3117355 ATGAGAAGAACTTATTGAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTAATACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
*
3117420 CTCGAGTGA
131 CTCGAGGGA
**
3117429 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCAT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-TGAGGGAGAAGAAGTTCAT
* * *
3117494 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAATTGAATCAGCAACACCTT
65 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
*
3117559 ACTCAAGGGA
130 ACTCGAGGGA
* *
3117569 CCAACATTTCCAGTGGATAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
3117634 ATGAGAAGAACTTGTTCAACCTTAGCT
66 ATGAGAAGAACTTGTTCAACCTTAGCT
3117661 TGTTTCCATC
Statistics
Matches: 473, Mismatches: 36, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
139 348 0.74
140 125 0.26
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (139 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
CTCGAGGGA
Found at i:3117872 original size:18 final size:18
Alignment explanation
Indices: 3117846--3117888 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3117836 TCATAATGAG
3117846 AAGAACTCGCCCGATAAA
1 AAGAACTCGCCCGATAAA
* *
3117864 AAGAGCTCGCCCGATAAG
1 AAGAACTCGCCCGATAAA
3117882 AAGAACT
1 AAGAACT
3117889 TGGAGCTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.12
Consensus pattern (18 bp):
AAGAACTCGCCCGATAAA
Found at i:3118693 original size:61 final size:61
Alignment explanation
Indices: 3118612--3118741 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 61
3118602 TTAGGATTTT
** * * * * *
3118612 GGGTAAATCATGCATCAAGTCCTC-CTTGTTTATTATGTTTTACGTTTTAGTTAT-TAGTTAA
1 GGGTAAATCACACATAAAGTCATCTC-TGTTTAGTATATTTCACGTTTTAGTT-TCTAGTTAA
*
3118673 GGGTAAATCACACATAAAGTCATCTCTGTTTAGTATATTTCATGTTTTAGTTTCTAGTTAA
1 GGGTAAATCACACATAAAGTCATCTCTGTTTAGTATATTTCACGTTTTAGTTTCTAGTTAA
3118734 GGGTAAAT
1 GGGTAAAT
3118742 TGCATACCAG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 1 0.02
61 57 0.97
62 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (61 bp):
GGGTAAATCACACATAAAGTCATCTCTGTTTAGTATATTTCACGTTTTAGTTTCTAGTTAA
Found at i:3119183 original size:15 final size:15
Alignment explanation
Indices: 3119165--3119212 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3119155 TATGTATTAC
3119165 ATATTTATTTTATGT
1 ATATTTATTTTATGT
3119180 ATA-TTATTATTATG-
1 ATATTTATT-TTATGT
*
3119194 -TATTTATTTTATTT
1 ATATTTATTTTATGT
3119208 ATATT
1 ATATT
3119213 ATTATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
13 6 0.21
14 10 0.36
15 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
ATATTTATTTTATGT
Found at i:3119188 original size:25 final size:25
Alignment explanation
Indices: 3119159--3119225 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 25
3119149 ATGTTTTATG
*
3119159 TATTACATATTTATTTTATGTATAT
1 TATTATATATTTATTTTATGTATAT
*
3119184 TATTATTATGTATTTATTTTATTTATAT
1 TATTA-TA--TATTTATTTTATGTATAT
3119212 TATTATATATTTAT
1 TATTATATATTTAT
3119226 ATAATACTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 12 0.32
26 1 0.03
27 2 0.05
28 22 0.59
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (25 bp):
TATTATATATTTATTTTATGTATAT
Found at i:3119191 original size:28 final size:28
Alignment explanation
Indices: 3119154--3119217 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
3119144 TAAGTATGTT
3119154 TTATGTATTACATATTTATTTTATGTATA
1 TTAT-TATTACATATTTATTTTATGTATA
** *
3119183 TTATTATTATGTATTTATTTTATTTATA
1 TTATTATTACATATTTATTTTATGTATA
3119211 TTATTAT
1 TTATTAT
3119218 ATATTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (28 bp):
TTATTATTACATATTTATTTTATGTATA
Found at i:3119209 original size:32 final size:35
Alignment explanation
Indices: 3119154--3119222 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 35
3119144 TAAGTATGTT
*
3119154 TTATGTATTACATATTTATTTTATGTATATTAT-TA
1 TTATGTATTACATATTTATTTTATAT-TATTATATA
*
3119189 TTATGTATT-TAT-TTTA-TTTATATTATTATATA
1 TTATGTATTACATATTTATTTTATATTATTATATA
3119221 TT
1 TT
3119223 TATATAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 6 0.19
32 10 0.32
33 4 0.13
34 2 0.06
35 9 0.29
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (35 bp):
TTATGTATTACATATTTATTTTATATTATTATATA
Found at i:3122047 original size:20 final size:20
Alignment explanation
Indices: 3122022--3122059 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3122012 TACATTGGGC
3122022 TATGAATATGAAAGTAAAGT
1 TATGAATATGAAAGTAAAGT
*
3122042 TATGAATCTGAAAGTAAA
1 TATGAATATGAAAGTAAA
3122060 CATACGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (20 bp):
TATGAATATGAAAGTAAAGT
Found at i:3122068 original size:20 final size:20
Alignment explanation
Indices: 3122025--3122070 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3122015 ATTGGGCTAT
* ** *
3122025 GAATATGAAAGTAAAGTTAT
1 GAATCTGAAAGTAAACATAC
3122045 GAATCTGAAAGTAAACATAC
1 GAATCTGAAAGTAAACATAC
3122065 GAATCT
1 GAATCT
3122071 AAAATAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (20 bp):
GAATCTGAAAGTAAACATAC
Found at i:3127629 original size:24 final size:25
Alignment explanation
Indices: 3127577--3127630 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
3127567 TCATATGATG
* ***
3127577 TAATATATCGAAAGTGACATTATTT
1 TAATAGATCGAAAGTGACATTAAGA
3127602 TAATAGAT-GAAAGTGACATTAAGA
1 TAATAGATCGAAAGTGACATTAAGA
3127626 TAATA
1 TAATA
3127631 TTTATTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (25 bp):
TAATAGATCGAAAGTGACATTAAGA
Found at i:3127892 original size:20 final size:19
Alignment explanation
Indices: 3127863--3127911 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 19
3127853 GCGAATATGT
3127863 AAATCGCAACACAGAAGTC
1 AAATCGCAACACAGAAGTC
3127882 AAATCCGCAACACAGAAGTC
1 AAAT-CGCAACACAGAAGTC
3127902 AAATTCGCAA
1 AAA-TCGCAA
3127912 AGCGCGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.14
20 23 0.82
21 1 0.04
ACGTcount: A:0.47, C:0.27, G:0.14, T:0.12
Consensus pattern (19 bp):
AAATCGCAACACAGAAGTC
Found at i:3128109 original size:22 final size:22
Alignment explanation
Indices: 3128059--3128109 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3128049 TAACTCTCTA
*
3128059 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATATC
** * *
3128081 CAACGACATTCTTCCCCATATC
1 CGGCGACATCCGTCCCCATATC
3128103 CGGCGAC
1 CGGCGAC
3128110 CCCCCTCTAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATATC
Found at i:3128474 original size:20 final size:20
Alignment explanation
Indices: 3128451--3128489 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3128441 TTTGAAACTT
3128451 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
**
3128471 AAATTCGTTACACGAAAAT
1 AAATTCGCAACACGAAAAT
3128490 CGCAAAGCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:3130090 original size:42 final size:42
Alignment explanation
Indices: 3130039--3130136 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
3130029 CCCCCACTTT
* * * * * *
3130039 GAGAACCATCACTTGATCAAGATGATTCTACAGCTCGACACC
1 GAGAGCCATCACCTGATCAAGACGATTATACACCTCCACACC
* *
3130081 GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACACC
1 GAGAGCCATCACCTGATCAAGACGATTATACACCTCCACACC
3130123 GAGAGCCATCACCT
1 GAGAGCCATCACCT
3130137 ATTCCATCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.18
Consensus pattern (42 bp):
GAGAGCCATCACCTGATCAAGACGATTATACACCTCCACACC
Found at i:3130397 original size:21 final size:21
Alignment explanation
Indices: 3130373--3130412 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3130363 ATCACAATGG
*
3130373 TACTTTACGTGGTGAGGTATC
1 TACTTTACGTGATGAGGTATC
*
3130394 TACTTTTCGTGATGAGGTA
1 TACTTTACGTGATGAGGTA
3130413 GCCGCTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (21 bp):
TACTTTACGTGATGAGGTATC
Found at i:3130742 original size:21 final size:21
Alignment explanation
Indices: 3130712--3130767 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
3130702 GATTCACCTG
3130712 TCATCATTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTC
*
3130733 TCATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTC
*
3130754 CCA-CTATTCAAGAG
1 TCATC-ATTCAAGAG
3130768 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:3132357 original size:20 final size:20
Alignment explanation
Indices: 3132334--3132516 Score: 102
Period size: 20 Copynumber: 8.8 Consensus size: 20
3132324 GAAAGTCAAA
*
3132334 TTCGCGTTGC-AATTTTTATT
1 TTCGCGTTGCGAA-TTTGATT
*
3132354 TTCGCG-TGTCGAATTCGATT
1 TTCGCGTTG-CGAATTTGATT
*
3132374 TTCGTGTTGCGAATTTGATT
1 TTCGCGTTGCGAATTTGATT
* *
3132394 TTCGCGTTGCGATTTTGACT
1 TTCGCGTTGCGAATTTGATT
**
3132414 TTCTTGTT-CGAATTTGACTT
1 TTCGCGTTGCGAATTTGA-TT
*** *
3132434 TCGCAACAATCGCAACGCGAATTTGACT
1 T--------TCGCGTTGCGAATTTGATT
*
3132462 TTCGCGTTGCGAATTTGAAT
1 TTCGCGTTGCGAATTTGATT
* **
3132482 TTCACGTTGCGAATTTGGCT
1 TTCGCGTTGCGAATTTGATT
*
3132502 TTCGAGTTGCGAATT
1 TTCGCGTTGCGAATT
3132517 CAAGGAAAAC
Statistics
Matches: 124, Mismatches: 26, Indels: 26
0.70 0.15 0.15
Matches are distributed among these distances:
19 10 0.08
20 97 0.78
21 4 0.03
28 4 0.03
29 9 0.07
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTGATT
Found at i:3132741 original size:18 final size:18
Alignment explanation
Indices: 3132718--3132753 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3132708 AAGCCAGTTG
* *
3132718 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTAATTT
3132736 TGATTGCGATTTTAATTT
1 TGATTGCGATTTTAATTT
3132754 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTAATTT
Found at i:3135055 original size:24 final size:24
Alignment explanation
Indices: 3135021--3135074 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3135011 CTGAAACATC
3135021 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3135045 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3135069 ATCAAA
1 ATCAAA
3135075 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3135088 original size:24 final size:24
Alignment explanation
Indices: 3135021--3135088 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
3135011 CTGAAACATC
* * *
3135021 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
3135045 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
3135069 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
3135089 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:3135831 original size:14 final size:15
Alignment explanation
Indices: 3135795--3135832 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3135785 GAAATCATTG
3135795 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
3135810 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
3135825 AAAAATTA
1 AAAAATTA
3135833 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:3135991 original size:20 final size:20
Alignment explanation
Indices: 3135966--3136017 Score: 72
Period size: 18 Copynumber: 2.7 Consensus size: 20
3135956 TACCCAAAAC
3135966 ATTTGTGTTGCGAAAATAAA
1 ATTTGTGTTGCGAAAATAAA
*
3135986 A-TT-TGTTGCGAAATTAAA
1 ATTTGTGTTGCGAAAATAAA
*
3136004 ATTCGTGTTGCGAA
1 ATTTGTGTTGCGAA
3136018 TTAGAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 15 0.54
19 3 0.11
20 10 0.36
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTGTGTTGCGAAAATAAA
Found at i:3136053 original size:20 final size:20
Alignment explanation
Indices: 3135970--3136056 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
3135960 CAAAACATTT
3135970 GTGTTGCGAAAATAAAATT-
1 GTGTTGCGAAAATAAAATTC
*
3135989 -TGTTGCGAAATTAAAATTC
1 GTGTTGCGAAAATAAAATTC
* *
3136008 GTGTTGCG-AATTAGAAAATC
1 GTGTTGCGAAAATA-AAATTC
** *
3136028 AAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAAATAAAATTC
3136048 GTGTTGCGA
1 GTGTTGCGA
3136057 TTTAGAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
18 17 0.31
19 5 0.09
20 30 0.55
21 3 0.05
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (20 bp):
GTGTTGCGAAAATAAAATTC
Found at i:3136075 original size:40 final size:40
Alignment explanation
Indices: 3135970--3136079 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 40
3135960 CAAAACATTT
* * * **
3135970 GTGTTGCGAA-AATAAAAT-TTGTTGCGAAATTAAAATTC
1 GTGTTGCGAATTAGAAAATCTTATTGCGAAAACAAAATTC
*
3136008 GTGTTGCGAATTAGAAAATC-AAGTTGCGAAAACAAAATTC
1 GTGTTGCGAATTAGAAAATCTTA-TTGCGAAAACAAAATTC
*
3136048 GTGTTGCGATTTAGAAAATCTTATTGCGAAAA
1 GTGTTGCGAATTAGAAAATCTTATTGCGAAAA
3136080 GGAAACTTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
38 10 0.17
39 6 0.10
40 43 0.72
41 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (40 bp):
GTGTTGCGAATTAGAAAATCTTATTGCGAAAACAAAATTC
Found at i:3136092 original size:40 final size:40
Alignment explanation
Indices: 3135990--3136067 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
3135980 AATAAAATTT
**
3135990 GTTGCGAAATTAAAATTCGTGTTGCGAATTAGAAAATCAA
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCAA
*
3136030 GTTGCGAAAACAAAATTCGTGTTGCGATTTAGAAAATC
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATC
3136068 TTATTGCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCAA
Found at i:3136117 original size:20 final size:20
Alignment explanation
Indices: 3136071--3136117 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3136061 GAAAATCTTA
* *
3136071 TTGCGAAAAGGAAACTTGTG
1 TTGCGAAAAAGAAACTTGCG
*
3136091 TTACGAAAAAGAAA-TTCGCG
1 TTGCGAAAAAGAAACTT-GCG
3136111 TTGCGAA
1 TTGCGAA
3136118 TTCATAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (20 bp):
TTGCGAAAAAGAAACTTGCG
Found at i:3136247 original size:20 final size:21
Alignment explanation
Indices: 3136151--3136259 Score: 102
Period size: 20 Copynumber: 5.4 Consensus size: 21
3136141 GAAATTTCGT
*
3136151 GTTGCTAATTTGGAAA-TCGC
1 GTTGCGAATTTGGAAACTCGC
* *
3136171 ATTGCGAATTTGGACA-TCGC
1 GTTGCGAATTTGGAAACTCGC
*
3136191 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTTGGAAACTCGC
* * *
3136212 GTTGAG-ATTGTAGAAACT-GG
1 GTTGCGAATT-TGGAAACTCGC
*
3136232 GTTGCGAATTTGGAAACT-GT
1 GTTGCGAATTTGGAAACTCGC
3136252 GTTGCGAA
1 GTTGCGAA
3136260 ATTAGAGTTC
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
20 56 0.76
21 18 0.24
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (21 bp):
GTTGCGAATTTGGAAACTCGC
Found at i:3136290 original size:19 final size:19
Alignment explanation
Indices: 3136268--3136309 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3136258 AAATTAGAGT
3136268 TCGCAACACGAATTTGAGA
1 TCGCAACACGAATTTGAGA
***
3136287 TCGCGTTACGAATTTGAGA
1 TCGCAACACGAATTTGAGA
3136306 TCGC
1 TCGC
3136310 GTTGCGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (19 bp):
TCGCAACACGAATTTGAGA
Found at i:3136310 original size:19 final size:19
Alignment explanation
Indices: 3136275--3136321 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3136265 AGTTCGCAAC
3136275 ACGAATTTGAGATCGCGTT
1 ACGAATTTGAGATCGCGTT
3136294 ACGAATTTGAGATCGCGTT
1 ACGAATTTGAGATCGCGTT
*
3136313 GCGAATTTG
1 ACGAATTTG
3136322 TTGGTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.32
Consensus pattern (19 bp):
ACGAATTTGAGATCGCGTT
Found at i:3136456 original size:18 final size:18
Alignment explanation
Indices: 3136435--3136482 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
3136425 TTAATTTTTT
3136435 TATAATTAATAATTAAAA
1 TATAATTAATAATTAAAA
*
3136453 TATAATTAA-AATCTAACA
1 TATAATTAATAAT-TAAAA
3136471 T-TAATT-ATAATT
1 TATAATTAATAATT
3136483 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.07
17 11 0.41
18 14 0.52
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAATTAATAATTAAAA
Found at i:3137230 original size:16 final size:16
Alignment explanation
Indices: 3137209--3137240 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3137199 GCAAGAACAT
3137209 ATAGTACAACATATAG
1 ATAGTACAACATATAG
3137225 ATAGTACAACATATAG
1 ATAGTACAACATATAG
3137241 TACGCATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (16 bp):
ATAGTACAACATATAG
Found at i:3139946 original size:18 final size:18
Alignment explanation
Indices: 3139914--3139948 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3139904 TTCATGTAAA
**
3139914 AATAAATATTTAAATTTT
1 AATAAATATAAAAATTTT
3139932 AATAAATATAAAAATTT
1 AATAAATATAAAAATTT
3139949 ATTAAACATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATATAAAAATTTT
Found at i:3141096 original size:170 final size:171
Alignment explanation
Indices: 3140814--3141155 Score: 677
Period size: 170 Copynumber: 2.0 Consensus size: 171
3140804 TTCAGCTATA
3140814 AACTTTCCAGTAAGAGACAAGTCAGTGCTTCCTTTTATAGTCGCTTGTGAATGGAGAAATGAATC
1 AACTTTCCAGTAAGAGACAAGTCAGTGCTTCCTTTTATAGTCGCTTGTGAATGGAGAAATGAATC
3140879 GAATGATGTTTTAAAAAGTTATGGCCCAAATTGTTAAACCAACAGCTAATAATCGAGGAAGGGTT
66 GAATGATGTTTTAAAAAGTTATGGCCCAAATTGTTAAACCAACAGCTAATAATCGAGGAAGGGTT
3140944 CTATCCTTGTCC-ACAAATTCGCCGCGTGATGCACGATGGC
131 CTATCCTTGTCCAACAAATTCGCCGCGTGATGCACGATGGC
3140984 AACTTTCCAGTAAGAGACAAGTCAGTGCTTCCTTTTATAGTCGCTTGTGAATGGAGAAATGAATC
1 AACTTTCCAGTAAGAGACAAGTCAGTGCTTCCTTTTATAGTCGCTTGTGAATGGAGAAATGAATC
3141049 GAATGATGTTTTAAAAAGTTATGGCCCAAATTGTTAAACCAACAGCTAATAATCGAGGAAGGGTT
66 GAATGATGTTTTAAAAAGTTATGGCCCAAATTGTTAAACCAACAGCTAATAATCGAGGAAGGGTT
3141114 CTATCCTTGTCCAACAAATTCGCCGCGTGATGCACGATGGC
131 CTATCCTTGTCCAACAAATTCGCCGCGTGATGCACGATGGC
3141155 A
1 A
3141156 CACGTCTCTA
Statistics
Matches: 171, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
170 142 0.83
171 29 0.17
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (171 bp):
AACTTTCCAGTAAGAGACAAGTCAGTGCTTCCTTTTATAGTCGCTTGTGAATGGAGAAATGAATC
GAATGATGTTTTAAAAAGTTATGGCCCAAATTGTTAAACCAACAGCTAATAATCGAGGAAGGGTT
CTATCCTTGTCCAACAAATTCGCCGCGTGATGCACGATGGC
Found at i:3152045 original size:46 final size:46
Alignment explanation
Indices: 3151995--3152282 Score: 267
Period size: 46 Copynumber: 6.3 Consensus size: 46
3151985 AAAATGAATT
* *
3151995 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAATGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
3152041 CATAAATGAAATGCATGAAAGGATGCCATAAATAAAATGAATGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGC
* *
3152092 C---AAT--AAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGC
**
3152139 CATAAATGAAATGCATGAAAGGATGCACAAAGGCATGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
3152184 CAT---T--AAGGCATGAAAGGATGCACTAAGGCATGAAAGGATGT
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
3152225 CATAACTGAAATGCATGAAAGGACGCATTAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
3152271 CATAAATGAAAT
1 CATAAATGAAAT
3152283 TAATGAATAA
Statistics
Matches: 206, Mismatches: 18, Indels: 36
0.79 0.07 0.14
Matches are distributed among these distances:
40 34 0.17
41 3 0.01
42 1 0.00
44 1 0.00
45 3 0.01
46 122 0.59
47 4 0.02
48 3 0.01
50 4 0.02
51 3 0.01
52 28 0.14
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.19
Consensus pattern (46 bp):
CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:3152079 original size:72 final size:72
Alignment explanation
Indices: 3151995--3152184 Score: 319
Period size: 72 Copynumber: 2.6 Consensus size: 72
3151985 AAAATGAATT
* * *
3151995 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAATGATGCCATAAATGAAATGCATGAA
1 CATAAATGAAATGCATGAAAGGATGCAATAAGGCATGAAAGGATGCCATAAATGAAATGCATGAA
3152060 AGGATGC
66 AGGATGC
* *
3152067 CATAAATAAAATGAATGAAAGGATGCAATAAGGCATGAAAGGATGCCATAAATGAAATGCATGAA
1 CATAAATGAAATGCATGAAAGGATGCAATAAGGCATGAAAGGATGCCATAAATGAAATGCATGAA
3152132 AGGATGC
66 AGGATGC
3152139 CATAAATGAAATGCATGAAAGGATGCACA-AAGGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCA-ATAAGGCATGAAAGGATGC
3152185 ATTAAGGCAT
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
72 109 0.99
73 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (72 bp):
CATAAATGAAATGCATGAAAGGATGCAATAAGGCATGAAAGGATGCCATAAATGAAATGCATGAA
AGGATGC
Found at i:3152085 original size:26 final size:26
Alignment explanation
Indices: 3152042--3152097 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
3152032 AAATGATGCC
3152042 ATAAATGAAATGCATGAAAGGATGCC
1 ATAAATGAAATGCATGAAAGGATGCC
* * *
3152068 ATAAATAAAATGAATGAAAGGATGCA
1 ATAAATGAAATGCATGAAAGGATGCC
3152094 ATAA
1 ATAA
3152098 GGCATGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.20
Consensus pattern (26 bp):
ATAAATGAAATGCATGAAAGGATGCC
Found at i:3152106 original size:20 final size:20
Alignment explanation
Indices: 3152081--3152275 Score: 140
Period size: 20 Copynumber: 8.8 Consensus size: 20
3152071 AATAAAATGA
3152081 ATGAAAGGATGCAATAAGGC
1 ATGAAAGGATGCAATAAGGC
*
3152101 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATG-C---AAT--AAGGC
*
3152127 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATG-C---AAT--AAGGC
3152153 ATGAAAGGATGCACA-AAGGC
1 ATGAAAGGATGCA-ATAAGGC
*
3152173 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCAATAAGGC
*
3152193 ATGAAAGGATGCACTAAGGC
1 ATGAAAGGATGCAATAAGGC
*
3152213 ATGAAAGGATGTCATAACTGAAATGC
1 ATGAAAGGATG-C--AA-T--AAGGC
* *
3152239 ATGAAAGGACGCATTAAGGC
1 ATGAAAGGATGCAATAAGGC
*
3152259 ATGAAAGGATGCCATAA
1 ATGAAAGGATGCAATAA
3152276 ATGAAATTAA
Statistics
Matches: 149, Mismatches: 12, Indels: 28
0.79 0.06 0.15
Matches are distributed among these distances:
20 81 0.54
21 2 0.01
22 2 0.01
23 3 0.02
24 4 0.03
25 2 0.01
26 55 0.37
ACGTcount: A:0.44, C:0.12, G:0.27, T:0.17
Consensus pattern (20 bp):
ATGAAAGGATGCAATAAGGC
Found at i:3152135 original size:26 final size:26
Alignment explanation
Indices: 3152099--3152164 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
3152089 ATGCAATAAG
3152099 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
3152125 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
3152151 GCATGAAAGGATGC
1 GCATGAAAGGATGC
3152165 ACAAAGGCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.18
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAAATGAAAT
Found at i:3157153 original size:29 final size:29
Alignment explanation
Indices: 3157121--3157192 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
3157111 GCGTGCTATA
3157121 TGCACTCGAAAGTGCCTCATAAAAATATT
1 TGCACTCGAAAGTGCCTCATAAAAATATT
* * * *
3157150 TGCACTTGAAAGTTCCTCGTAGAAATATT
1 TGCACTCGAAAGTGCCTCATAAAAATATT
* *
3157179 TGCAATCGGAAGTG
1 TGCACTCGAAAGTG
3157193 TCTCGTAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (29 bp):
TGCACTCGAAAGTGCCTCATAAAAATATT
Found at i:3157197 original size:29 final size:29
Alignment explanation
Indices: 3157121--3157202 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
3157111 GCGTGCTATA
* * * *
3157121 TGCACTCGAAAGTGCCTCATAAAAATATT
1 TGCAATCGAAAGTTCCTCGTAGAAATATT
* *
3157150 TGCACTTGAAAGTTCCTCGTAGAAATATT
1 TGCAATCGAAAGTTCCTCGTAGAAATATT
*
3157179 TGCAATCGGAAGTGT-CTCGTAGAA
1 TGCAATCGAAAGT-TCCTCGTAGAA
3157203 TTGTACCATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 44 0.98
30 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (29 bp):
TGCAATCGAAAGTTCCTCGTAGAAATATT
Found at i:3161790 original size:12 final size:12
Alignment explanation
Indices: 3161755--3161797 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
3161745 TTTAAAAAAA
*
3161755 ATTAACTAATA-
1 ATTAAATAATAT
* *
3161766 ATTAATTATTAT
1 ATTAAATAATAT
3161778 ATTAAATAATAT
1 ATTAAATAATAT
3161790 ATTAAATA
1 ATTAAATA
3161798 TTTATGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTAAATAATAT
Found at i:3162862 original size:128 final size:127
Alignment explanation
Indices: 3162426--3162869 Score: 840
Period size: 128 Copynumber: 3.5 Consensus size: 127
3162416 TAATCGGAGT
*
3162426 ACTATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
3162491 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCA-TCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
3162554 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
3162619 CATTGCCCTATTATG---TCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCATCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
3162678 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
3162743 CATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCA-TCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
3162806 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
3162870 GAGGAGAATA
Statistics
Matches: 311, Mismatches: 1, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
124 124 0.40
128 187 0.60
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (127 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCATCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:3164176 original size:19 final size:20
Alignment explanation
Indices: 3164154--3164191 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3164144 TTTATTTAAT
3164154 ATTTATTTT-AAAA-TAAAAG
1 ATTT-TTTTGAAAATTAAAAG
3164173 ATTTTTTTGAAAATTAAAA
1 ATTTTTTTGAAAATTAAAA
3164192 TAAAAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTTTTTGAAAATTAAAAG
Found at i:3164263 original size:3 final size:3
Alignment explanation
Indices: 3164255--3164284 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3164245 AAACAAGTAC
3164255 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3164285 GGGCAGACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3167826 original size:40 final size:40
Alignment explanation
Indices: 3167777--3167859 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
3167767 CTGATAAAAA
3167777 TTTTGCTTCATTACAAGTCCGTATGGGCCATGTTATAAAT
1 TTTTGCTTCATTACAAGTCCGTATGGGCCATGTTATAAAT
3167817 TTTTGCTTCATTACAAGTCCGTATGGGCCATGTTATAAAT
1 TTTTGCTTCATTACAAGTCCGTATGGGCCATGTTATAAAT
3167857 TTT
1 TTT
3167860 GTGCATGGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (40 bp):
TTTTGCTTCATTACAAGTCCGTATGGGCCATGTTATAAAT
Found at i:3170464 original size:14 final size:14
Alignment explanation
Indices: 3170431--3170465 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3170421 TTGTTTCACT
*
3170431 GAAAACGTTTTTCG
1 GAAAATGTTTTTCG
3170445 GAAAATGTTTTTCG
1 GAAAATGTTTTTCG
*
3170459 TAAAATG
1 GAAAATG
3170466 AATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (14 bp):
GAAAATGTTTTTCG
Found at i:3170610 original size:27 final size:26
Alignment explanation
Indices: 3170579--3170657 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 26
3170569 TTATTACAAA
3170579 TATTAAAATACAATAAATAATATTATT
1 TATTAAAATAC-ATAAATAATATTATT
* * *
3170606 TATTATAA-AC-TTAATATTATTA-T
1 TATTAAAATACATAAATAATATTATT
*
3170629 T-TTAAAATA-TTAAAATAAT-TTATT
1 TATTAAAATACAT-AAATAATATTATT
3170653 TATTA
1 TATTA
3170658 TTAAAATATT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
22 5 0.12
23 7 0.17
24 17 0.41
25 3 0.07
26 2 0.05
27 7 0.17
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTAAAATACATAAATAATATTATT
Found at i:3170622 original size:21 final size:20
Alignment explanation
Indices: 3170596--3170634 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3170586 ATACAATAAA
3170596 TAATATTATTTATTATAAACT
1 TAATATTA-TTATTATAAACT
*
3170617 TAATATTATTATTTTAAA
1 TAATATTATTATTATAAA
3170635 ATATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATATTATTATTATAAACT
Found at i:3170675 original size:14 final size:14
Alignment explanation
Indices: 3170652--3170697 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3170642 AATAATTTAT
3170652 TTATTATTAAAATA
1 TTATTATTAAAATA
* *
3170666 TTATTTTTAAAATT
1 TTATTATTAAAATA
*
3170680 TTATTAATAAAAATA
1 TTATT-ATTAAAATA
3170695 TTA
1 TTA
3170698 ATATGGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTATTATTAAAATA
Found at i:3170681 original size:50 final size:52
Alignment explanation
Indices: 3170558--3170682 Score: 120
Period size: 47 Copynumber: 2.5 Consensus size: 52
3170548 GATGAATTTT
*
3170558 TTAAAA-ATTATTTATTACAAATATTAAAATACAATAAATAATATTATTTATTA
1 TTAAAATATTATTT-TTA-AAATTTTAAAATACAATAAATAATATTATTTATTA
* * * **
3170611 -TAAACTTAATATTATT---ATTTTAAAATATTA-AAATAAT-TTATTTATTA
1 TTAAA-ATATTATTTTTAAAATTTTAAAATACAATAAATAATATTATTTATTA
3170658 TTAAAATATTATTTTTAAAATTTTA
1 TTAAAATATTATTTTTAAAATTTTA
3170683 TTAATAAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
47 18 0.32
48 11 0.19
49 11 0.19
50 6 0.11
52 4 0.07
53 2 0.04
54 5 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (52 bp):
TTAAAATATTATTTTTAAAATTTTAAAATACAATAAATAATATTATTTATTA
Found at i:3170873 original size:19 final size:19
Alignment explanation
Indices: 3170805--3170885 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
3170795 TTAAATATCT
3170805 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
3170824 TTATTAGATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
3170843 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
3170863 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
3170881 -TATTA
1 TTATTA
3170886 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:3172408 original size:69 final size:71
Alignment explanation
Indices: 3172237--3172410 Score: 199
Period size: 75 Copynumber: 2.4 Consensus size: 71
3172227 ACTCTTTCCT
* * **
3172237 GTGTGAGACACTTTAACCCTTCGGGGCTCCCGTGCGAGACATTCGAAATGATTATGATTATGATT
1 GTGTGAGACACTCTAACCCTTCGGGGCTCTCGTGCGAGACACCCGAAATGATTATGATTATG---
*
3172302 ACGTGATCCT
63 A-GTGATCCC
** * *
3172312 GTACGAGACATTCTAACCATTCGGGGCTCTCGTGCGAGACACCCGAAATGATTATGATTA-G-GT
1 GTGTGAGACACTCTAACCCTTCGGGGCTCTCGTGCGAGACACCCGAAATGATTATGATTATGAGT
*
3172375 GCTCCC
66 GATCCC
*
3172381 GTGTGAGACACTCTAACCCTTCAGGGCTCT
1 GTGTGAGACACTCTAACCCTTCGGGGCTCT
3172411 TGTAACGCCA
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
69 31 0.37
74 1 0.01
75 52 0.62
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (71 bp):
GTGTGAGACACTCTAACCCTTCGGGGCTCTCGTGCGAGACACCCGAAATGATTATGATTATGAGT
GATCCC
Found at i:3175975 original size:53 final size:52
Alignment explanation
Indices: 3175906--3176031 Score: 128
Period size: 53 Copynumber: 2.3 Consensus size: 52
3175896 TCTCGGAGCC
* * *
3175906 AGGGTGTATCGGTACATAAGCCAGTATATCGATACACAAAATGCATTCGATG-T
1 AGGGGGTATCGATACATAAG--AGTATATCGATACACAAAATACATTCGATGTT
* * * *
3175959 AGGGGGTATCGATACATCCAAGAGTGTATCGGTACCCAAATTACATTCGATGTT
1 AGGGGGTATCGATACAT--AAGAGTATATCGATACACAAAATACATTCGATGTT
*
3176013 GGGGGTGTATCGATACATA
1 AGGGG-GTATCGATACATA
3176032 CAAGAGTGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
53 41 0.67
54 5 0.08
55 15 0.25
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (52 bp):
AGGGGGTATCGATACATAAGAGTATATCGATACACAAAATACATTCGATGTT
Found at i:3176660 original size:19 final size:18
Alignment explanation
Indices: 3176619--3176671 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
3176609 TGCAAAAATT
**
3176619 AATCAAACCAATATAAATT
1 AATCAAACCAA-ATAAAAC
3176638 AATCAAACCAAATACAAAC
1 AATCAAACCAAATA-AAAC
3176657 AATCAAAACCAAATA
1 AATC-AAACCAAATA
3176672 TATATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 3 0.10
19 17 0.57
20 10 0.33
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (18 bp):
AATCAAACCAAATAAAAC
Found at i:3183580 original size:79 final size:79
Alignment explanation
Indices: 3183449--3183606 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
3183439 GGTTTAACAT
3183449 AGAAGAATTAAGTGAATAATTGATGATTTTCGGGGTTAAAATACAATTTATGGGTAGAGGGAACC
1 AGAAGAATTAAGTGAATAATTGATGATTTTCGGGGTTAAAATACAATTTATGGGTAGAGGGAACC
3183514 GATACCCTATGAAG
66 GATACCCTATGAAG
3183528 AGAAGAATTAAGTGAATAATTGATGATTTTCGGGGTTAAAATACAATTTATGGGTAGAGGGAACC
1 AGAAGAATTAAGTGAATAATTGATGATTTTCGGGGTTAAAATACAATTTATGGGTAGAGGGAACC
3183593 GATACCCTATGAAG
66 GATACCCTATGAAG
3183607 GGAATCGATT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (79 bp):
AGAAGAATTAAGTGAATAATTGATGATTTTCGGGGTTAAAATACAATTTATGGGTAGAGGGAACC
GATACCCTATGAAG
Found at i:3184413 original size:38 final size:38
Alignment explanation
Indices: 3184370--3184581 Score: 325
Period size: 38 Copynumber: 5.6 Consensus size: 38
3184360 ATAAGACATG
* *
3184370 TGACAGGTCCTTCGGGACACATATTACATCCTTCAGGA
1 TGACAGGTCCTTCGGGACACAGATTACATCCTTCGGGA
*
3184408 TGACAGGTCCTTCGGGACACAAATTACATCCTTCGGGA
1 TGACAGGTCCTTCGGGACACAGATTACATCCTTCGGGA
*
3184446 TGACAGGTCCTTCGGGACACAGATTACATCCTTTGGGA
1 TGACAGGTCCTTCGGGACACAGATTACATCCTTCGGGA
* *
3184484 TGACAGGTCTTTCGGGACACAGATGACATCCTTCGGGGA
1 TGACAGGTCCTTCGGGACACAGATTACATCCTTC-GGGA
* * *
3184523 TGATAGGTCTTTCGGGACACAGATGACATCCTTCGGGA
1 TGACAGGTCCTTCGGGACACAGATTACATCCTTCGGGA
*
3184561 TGATAGGTCCTTCGGGACACA
1 TGACAGGTCCTTCGGGACACA
3184582 ATTTATACGA
Statistics
Matches: 164, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
38 127 0.77
39 37 0.23
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (38 bp):
TGACAGGTCCTTCGGGACACAGATTACATCCTTCGGGA
Found at i:3184508 original size:23 final size:23
Alignment explanation
Indices: 3184482--3184550 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
3184472 CATCCTTTGG
3184482 GATGACAGGTCTTTCGGGACACA
1 GATGACAGGTCTTTCGGGACACA
*
3184505 GATGACA--TCCTTCGGG-----
1 GATGACAGGTCTTTCGGGACACA
*
3184521 GATGATAGGTCTTTCGGGACACA
1 GATGACAGGTCTTTCGGGACACA
3184544 GATGACA
1 GATGACA
3184551 TCCTTCGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
16 6 0.17
18 8 0.23
21 8 0.23
23 13 0.37
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (23 bp):
GATGACAGGTCTTTCGGGACACA
Found at i:3184571 original size:115 final size:114
Alignment explanation
Indices: 3184370--3184581 Score: 334
Period size: 115 Copynumber: 1.9 Consensus size: 114
3184360 ATAAGACATG
* * *
3184370 TGACAGGTCCTTCGGGACACATATTACATCCTTCAGGATGACAGGTCCTTCGGGACACAAATTAC
1 TGACAGGTCCTTCGGGACACAGATGACATCCTTCAGGATGACAGGTCCTTCGGGACACAAATGAC
3184435 ATCCTTCGGGATGACAGGTCCTTCGGGACACAGATTACATCCTTTGGGA
66 ATCCTTCGGGATGACAGGTCCTTCGGGACACAGATTACATCCTTTGGGA
* * * * *
3184484 TGACAGGTCTTTCGGGACACAGATGACATCCTTCGGGGATGATAGGTCTTTCGGGACACAGATGA
1 TGACAGGTCCTTCGGGACACAGATGACATCCTTC-AGGATGACAGGTCCTTCGGGACACAAATGA
*
3184549 CATCCTTCGGGATGATAGGTCCTTCGGGACACA
65 CATCCTTCGGGATGACAGGTCCTTCGGGACACA
3184582 ATTTATACGA
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
114 31 0.35
115 57 0.65
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (114 bp):
TGACAGGTCCTTCGGGACACAGATGACATCCTTCAGGATGACAGGTCCTTCGGGACACAAATGAC
ATCCTTCGGGATGACAGGTCCTTCGGGACACAGATTACATCCTTTGGGA
Found at i:3186891 original size:55 final size:55
Alignment explanation
Indices: 3186750--3186895 Score: 168
Period size: 55 Copynumber: 2.7 Consensus size: 55
3186740 CTCAGAGCCA
* * * * *
3186750 GGGGTGTATCGGTACAT-CAGCCAGTGTATCGATACACAAAATGCATTCGATGTAG
1 GGGGTGTATCGATACATCCA-ACAGTGTATCGGTACCCAAAATACATTCGATGTAG
* * * * * *
3186805 AGCGTGTATTGATACATCCAAGAGTGTATCGGTACCCAAATTACATTCGATGTTG
1 GGGGTGTATCGATACATCCAACAGTGTATCGGTACCCAAAATACATTCGATGTAG
*
3186860 GGGGTGTATCGATACATCCAATAGTGTATCGGTACC
1 GGGGTGTATCGATACATCCAACAGTGTATCGGTACC
3186896 TCCCTTTGTA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
55 73 0.97
56 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (55 bp):
GGGGTGTATCGATACATCCAACAGTGTATCGGTACCCAAAATACATTCGATGTAG
Found at i:3189777 original size:45 final size:45
Alignment explanation
Indices: 3189725--3189814 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
3189715 GTAAAATTAC
3189725 AGTCTAGGCCCTCCACCTTTTACTACAAGCTTAAAAATCTCATTT
1 AGTCTAGGCCCTCCACCTTTTACTACAAGCTTAAAAATCTCATTT
3189770 AGTCTAGGCCCTCCACCTTTTACTACAAGCTTAAAAATCTCATTT
1 AGTCTAGGCCCTCCACCTTTTACTACAAGCTTAAAAATCTCATTT
3189815 TTATCTTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (45 bp):
AGTCTAGGCCCTCCACCTTTTACTACAAGCTTAAAAATCTCATTT
Found at i:3191841 original size:23 final size:23
Alignment explanation
Indices: 3191815--3191859 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3191805 CACCACAGCT
*
3191815 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
3191838 CGTAGAATTGTACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
3191860 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:3192103 original size:155 final size:149
Alignment explanation
Indices: 3191827--3192147 Score: 554
Period size: 155 Copynumber: 2.1 Consensus size: 149
3191817 TATAATTGCA
*
3191827 CCGAAGTG-CCGCGTAGAATTGTACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAA-TGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
3191891 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
3191956 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
3191976 CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCAGGACCACA
1 CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCAT----A--AGGACCACA
3192041 TAGAATTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACAC
60 TAGAATTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACAC
3192106 ATGTTCCAAAGAATATACATATGTC
125 ATGTTCCAAAGAATATACATATGTC
*
3192131 CCGAAGGACCGCGTAGA
1 CCGAATGACCGCGTAGA
3192148 CCCTCGACTC
Statistics
Matches: 163, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
148 2 0.01
149 45 0.28
153 1 0.01
155 115 0.71
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAATGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:3193033 original size:18 final size:18
Alignment explanation
Indices: 3193012--3193046 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3193002 TCCCATCTAG
3193012 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
3193030 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
3193047 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:3197012 original size:23 final size:23
Alignment explanation
Indices: 3196986--3197030 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3196976 CACCACAGCT
*
3196986 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
3197009 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
3197031 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:3197282 original size:155 final size:149
Alignment explanation
Indices: 3197006--3197318 Score: 554
Period size: 155 Copynumber: 2.1 Consensus size: 149
3196996 CACCGAAGTG
3197006 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
3197071 AATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAAT
*
3197136 ATACATATGTCCCAAATGA
131 ATACATATGTCCCAAAGGA
3197155 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCAGTACCACATAGAATTC
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAA-G----G-ACCACATAGAATTC
3197220 CTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCA
60 CTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCA
*
3197285 AAGAATATACATATGTCCCGAAGGA
125 AAGAATATACATATGTCCCAAAGGA
3197310 CCGCGTAGA
1 CCGCGTAGA
3197319 CCCTCGACTC
Statistics
Matches: 156, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
149 43 0.28
150 1 0.01
154 1 0.01
155 111 0.71
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAAT
ATACATATGTCCCAAAGGA
Found at i:3198214 original size:18 final size:18
Alignment explanation
Indices: 3198193--3198227 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3198183 TCCCATCTAG
3198193 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
3198211 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
3198228 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:3198832 original size:21 final size:21
Alignment explanation
Indices: 3198808--3198852 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3198798 TGTTGTTCGT
* *
3198808 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3198829 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3198850 TTG
1 TTG
3198853 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3201836 original size:58 final size:58
Alignment explanation
Indices: 3201746--3201863 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
3201736 TTATCTCATC
3201746 ATAGGTAAGTACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTG
1 ATAGGTAAGTACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTG
3201804 ATAGGTAAGTACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTG
1 ATAGGTAAGTACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTG
3201862 AT
1 AT
3201864 TGAACAACAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (58 bp):
ATAGGTAAGTACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTG
Found at i:3201876 original size:58 final size:58
Alignment explanation
Indices: 3201756--3201876 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 58
3201746 ATAGGTAAGT
* **
3201756 ACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTGATAGGTAAGT
1 ACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTGATAGGAAAAC
*
3201814 ACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTGAT-TGAACAAC
1 ACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTGATAGGAA-AAC
3201872 ACAAA
1 ACAAA
3201877 CAATGCAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
57 2 0.03
58 56 0.97
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (58 bp):
ACAAAGGCATGACAATTGTTTATTTGTCTAAATGTCATGGAAAGCTTGATAGGAAAAC
Found at i:3202302 original size:20 final size:19
Alignment explanation
Indices: 3202277--3202314 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3202267 AATAAGAGAA
*
3202277 ACTAAATTAAATAAATAAAG
1 ACTAAAATAAA-AAATAAAG
3202297 ACTAAAATAAAAAATAAA
1 ACTAAAATAAAAAATAAA
3202315 AATAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (19 bp):
ACTAAAATAAAAAATAAAG
Found at i:3205298 original size:17 final size:16
Alignment explanation
Indices: 3205276--3205309 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3205266 TAAAAACAGT
3205276 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
3205293 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
3205309 A
1 A
3205310 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:3205829 original size:24 final size:24
Alignment explanation
Indices: 3205785--3205831 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3205775 ATAAAGAACC
*
3205785 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3205809 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
3205832 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3209121 original size:19 final size:20
Alignment explanation
Indices: 3209099--3209142 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3209089 GAGAAAAGGT
*
3209099 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAC
*
3209118 AAAAATTAATAATGAAAGAC
1 AAAAGTTAATAATGAAAGAC
3209138 AAAAG
1 AAAAG
3209143 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAC
Found at i:3209880 original size:150 final size:146
Alignment explanation
Indices: 3209603--3209901 Score: 546
Period size: 150 Copynumber: 2.0 Consensus size: 146
3209593 TCATACGCTG
3209603 GCCATGACCTTGAAGATCTCCCATTGTCTATTCTCTTGATGTCAACAGCTCCATGGGGATAGACA
1 GCCATGACCTTGAAGATCTCCCATTGTCTATTCTCTTGATGTCAACAGCTCCATGGGGATAGACA
3209668 TATGCACCAAATGGCCTGACCATCGAGATTTTAGCTTCCCAGGAAAGAGTTTAAGTCTAGAGTTG
66 TATGCACCAAATGGCCTGACCATCGAGATTTTAGCTTCCCAGGAAAGAGTTTAAGTCTAGAGTTG
3209733 TAAAGCAAGACTT-TT
131 TAAAGCAAGACTTGTT
3209748 GCCATGACCTTGAAGATCTTCCCATTGTCTATTCTCTTGATGTCAACAGCTCCATGGGGATAGAC
1 GCCATGACCTTGAAGATC-TCCCATTGTCTATTCTCTTGATGTCAACAGCTCCATGGGGATAGAC
3209813 ATAATGCACCTCAAATGGCCCTGACCATCGAGATTTTAGCTTCCCAGGAAAGAGTTTAAGTCTAG
65 AT-ATGCA-C-CAAATGG-CCTGACCATCGAGATTTTAGCTTCCCAGGAAAGAGTTTAAGTCTAG
3209878 AGTTGTAAAGCAAGACTTGTT
126 AGTTGTAAAGCAAGACTTGTT
3209899 GCC
1 GCC
3209902 CCACATGAAA
Statistics
Matches: 148, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
145 18 0.12
146 48 0.32
147 5 0.03
148 1 0.01
149 7 0.05
150 64 0.43
151 5 0.03
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (146 bp):
GCCATGACCTTGAAGATCTCCCATTGTCTATTCTCTTGATGTCAACAGCTCCATGGGGATAGACA
TATGCACCAAATGGCCTGACCATCGAGATTTTAGCTTCCCAGGAAAGAGTTTAAGTCTAGAGTTG
TAAAGCAAGACTTGTT
Found at i:3214700 original size:21 final size:21
Alignment explanation
Indices: 3214674--3214716 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3214664 ACCAAGCTCT
3214674 GCTCGGTCACGCAATGAATAC
1 GCTCGGTCACGCAATGAATAC
3214695 GCTCGGTCACGCAATGAATAC
1 GCTCGGTCACGCAATGAATAC
3214716 G
1 G
3214717 GAAAAAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
GCTCGGTCACGCAATGAATAC
Found at i:3215208 original size:17 final size:18
Alignment explanation
Indices: 3215186--3215220 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3215176 CAAGTAAACT
3215186 ATACAAAA-AAAATAAAA
1 ATACAAAACAAAATAAAA
3215203 ATACAAAACAAAATAAAA
1 ATACAAAACAAAATAAAA
3215221 TAAAATGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (18 bp):
ATACAAAACAAAATAAAA
Found at i:3215623 original size:17 final size:16
Alignment explanation
Indices: 3215601--3215634 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3215591 TAAAAACATT
3215601 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
3215618 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
3215634 A
1 A
3215635 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:3216153 original size:24 final size:24
Alignment explanation
Indices: 3216109--3216155 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3216099 ATAAAGAACC
*
3216109 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
3216133 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
3216156 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:3216635 original size:24 final size:24
Alignment explanation
Indices: 3216608--3216658 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3216598 CAAGTGGCGT
3216608 GGTCCATTGGCAGCTCTGGCAGGC
1 GGTCCATTGGCAGCTCTGGCAGGC
3216632 GGTCCATTGGCAGCTCTGGCAGGC
1 GGTCCATTGGCAGCTCTGGCAGGC
3216656 GGT
1 GGT
3216659 TACAACAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.27, G:0.39, T:0.22
Consensus pattern (24 bp):
GGTCCATTGGCAGCTCTGGCAGGC
Found at i:3223408 original size:12 final size:12
Alignment explanation
Indices: 3223393--3223438 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
3223383 CGGTTTTTTT
*
3223393 ACCGGATAAAAA
1 ACCGGTTAAAAA
3223405 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
3223420 ACCGGTTAAAAA
1 ACCGGTTAAAAA
3223432 ACCGGTT
1 ACCGGTT
3223439 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:3223420 original size:15 final size:13
Alignment explanation
Indices: 3223399--3223439 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
3223389 TTTTACCGGA
3223399 TAAAAAACCGGTT
1 TAAAAAACCGGTT
3223412 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
3223426 TAAAAAACCGGTT
1 TAAAAAACCGGTT
3223439 T
1 T
3223440 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:3225629 original size:21 final size:21
Alignment explanation
Indices: 3225613--3225652 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3225603 GTTTATTTAT
3225613 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
3225634 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
3225653 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:3225700 original size:33 final size:33
Alignment explanation
Indices: 3225647--3225745 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
3225637 TTTGTTTCAA
3225647 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3225679 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
3225712 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3225745 T
1 T
3225746 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:3225774 original size:13 final size:13
Alignment explanation
Indices: 3225731--3225785 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3225721 TTGGAAGTAT
3225731 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
3225744 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
3225758 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
3225771 TTAAGTATTTGAA
1 TTAAGTATTTCAA
3225784 TT
1 TT
3225786 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:3226007 original size:21 final size:21
Alignment explanation
Indices: 3225981--3226037 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
3225971 TAGAGCGTGG
*
3225981 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
3226002 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
3226023 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
3226038 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:3235000 original size:31 final size:30
Alignment explanation
Indices: 3234965--3235044 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
3234955 GTCCGATTTA
*
3234965 ATACCTAAAATTTTA-TTTTATCCCCAAAAAC
1 ATACCTAACATTTTAGTTTT-T-CCCAAAAAC
* *
3234996 ATACCTAACA-TTTAGTTTTTTCCAAAAGC
1 ATACCTAACATTTTAGTTTTTCCCAAAAAC
3235025 ATACCTAACA-TTTAGTTTTT
1 ATACCTAACATTTTAGTTTTT
3235045 GATTCATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 27 0.60
30 5 0.11
31 13 0.29
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (30 bp):
ATACCTAACATTTTAGTTTTTCCCAAAAAC
Found at i:3235044 original size:28 final size:29
Alignment explanation
Indices: 3234988--3235044 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
3234978 TATTTTATCC
3234988 CCAAAAACATACCTAACATTTAGTTTTTT
1 CCAAAAACATACCTAACATTTAGTTTTTT
*
3235017 CCAAAAGCATACCTAACATTTAGTTTTT
1 CCAAAAACATACCTAACATTTAGTTTTT
3235045 GATTCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (29 bp):
CCAAAAACATACCTAACATTTAGTTTTTT
Found at i:3236202 original size:20 final size:19
Alignment explanation
Indices: 3236144--3236211 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 19
3236134 GAATGGTACA
3236144 GATACCCCCCATA-GGTATC
1 GATA-CCCCCATATGGTATC
3236163 GATACCCCCATGCAATGGTATC
1 GATACCCCCAT---ATGGTATC
*
3236185 GATACCCCTCATATGGTACC
1 GATACCCC-CATATGGTATC
3236205 GATACCC
1 GATACCC
3236212 TAAGGCATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 7 0.16
19 4 0.09
20 14 0.33
21 1 0.02
22 14 0.33
23 3 0.07
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.22
Consensus pattern (19 bp):
GATACCCCCATATGGTATC
Found at i:3252235 original size:140 final size:139
Alignment explanation
Indices: 3251983--3252292 Score: 405
Period size: 140 Copynumber: 2.2 Consensus size: 139
3251973 CCTTAGCCCG
* * *
3251983 AGGTTCCAAATTAATTATCA-GATTCAATAAATTATTAAAATTGGTTAAGTGTAATATTATAGCA
1 AGGTTCCAATTTAATTAT-ATGATTCAATAAATTATTAAAATTAGTTAAGTGTAATATTAAAGCA
* *
3252047 TTCACCTTAGGTTTAATTTCACCTTAGTCCATTTAATTTAGGTGAATTTTTAATTTGGTCCTCGT
65 TTCACCTTAGATTTAATTTCACCTTAGTCCACTTAATTTAGGTGAATTTTTAATTTGGTCCTCG-
*
3252112 CTTTATGCCTA
129 ATTTATGCCTA
* *
3252123 AGGTTCCACTTTAATTATATGATTCAATAAATTGA-TAAAATTAGTTAAGTTTAATATTAAAGTC
1 AGGTTCCAATTTAATTATATGATTCAATAAATT-ATTAAAATTAGTTAAGTGTAATATTAAAG-C
* *
3252187 -TTTACGTTAGATTTAATTTCACCTTTAGT-CACTTAATTTAGGTGAATTTTTAATTTGGTCCTC
64 ATTCACCTTAGATTTAATTTCACC-TTAGTCCACTTAATTTAGGTGAATTTTTAATTTGGTCCTC
*
3252250 GATTTATGCCTG
128 GATTTATGCCTA
* * *
3252262 AGGTTCCATTTTGATTAT-TCAATTCAATAAA
1 AGGTTCCAATTTAATTATAT-GATTCAATAAA
3252293 ATGGTTAAAT
Statistics
Matches: 151, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
138 1 0.01
139 36 0.24
140 107 0.71
141 7 0.05
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (139 bp):
AGGTTCCAATTTAATTATATGATTCAATAAATTATTAAAATTAGTTAAGTGTAATATTAAAGCAT
TCACCTTAGATTTAATTTCACCTTAGTCCACTTAATTTAGGTGAATTTTTAATTTGGTCCTCGAT
TTATGCCTA
Found at i:3252640 original size:138 final size:135
Alignment explanation
Indices: 3252361--3252616 Score: 307
Period size: 138 Copynumber: 1.9 Consensus size: 135
3252351 ATGTAGTTCC
* * *
3252361 TTAATTTAGGTGAATATTCAAAATGGTCCCTGTCATAGCTTGGGGTTCCAAATTGATTATTCGAT
1 TTAATTTAGGTGAATATTCAAAATGGTCCCTATCATAGCTTGGGGTTCCAAATGGATTATTCAAT
* * * * ** *
3252426 TCAATAAATTGTTAAATGTGGTTAGGTTTTAATATTAGATCCTTCATCTTAGTTTTCATTTTACT
66 TCAATAAATTGTAAAATGTGGTTAGATTTTAATATTAAAGCCAACATCTTAGTTTCCATTTTA--
*
3252491 TTAGTCCT
129 -TAGTCAT
* * **
3252499 TTAATTTAGGTGAATATTCAAAATGGTCTCTATTATTTCTTGGGGTTCCAAATGGATTATTCAAT
1 TTAATTTAGGTGAATATTCAAAATGGTCCCTATCATAGCTTGGGGTTCCAAATGGATTATTCAAT
* *
3252564 TCAATGAAATTTGTAAAAT-TTGTTAGATTTTAATATTAAAGCCAACATTTTAG
66 TCAAT-AAA-TTGTAAAATGTGGTTAGATTTTAATATTAAAGCCAACATCTTAG
3252617 GTTTAGCCCT
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
138 63 0.62
139 30 0.30
140 8 0.08
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (135 bp):
TTAATTTAGGTGAATATTCAAAATGGTCCCTATCATAGCTTGGGGTTCCAAATGGATTATTCAAT
TCAATAAATTGTAAAATGTGGTTAGATTTTAATATTAAAGCCAACATCTTAGTTTCCATTTTATA
GTCAT
Found at i:3255771 original size:7 final size:7
Alignment explanation
Indices: 3255759--3255793 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
3255749 ACGCGCATAA
3255759 GAATATT
1 GAATATT
3255766 GAATATT
1 GAATATT
3255773 GAATATT
1 GAATATT
*
3255780 GCATA-T
1 GAATATT
3255786 GAATATT
1 GAATATT
3255793 G
1 G
3255794 TTCAACTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (7 bp):
GAATATT
Found at i:3257184 original size:33 final size:33
Alignment explanation
Indices: 3257140--3257203 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
3257130 CATCGTGGTT
3257140 GTTGTTCCCGTGTCTTCTCCTTGAGTTGTCGTC
1 GTTGTTCCCGTGTCTTCTCCTTGAGTTGTCGTC
* * *
3257173 GTTGTTGCCGTGTTTTCTCCTTGGGTTGTCG
1 GTTGTTCCCGTGTCTTCTCCTTGAGTTGTCG
3257204 GCTCTTGCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.02, C:0.23, G:0.28, T:0.47
Consensus pattern (33 bp):
GTTGTTCCCGTGTCTTCTCCTTGAGTTGTCGTC
Found at i:3260062 original size:33 final size:32
Alignment explanation
Indices: 3260019--3260080 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
3260009 TTTTATTCAT
*
3260019 TATTTTTATTA-CATTAATTTCATATAATTGTA
1 TATTTTTATTATCATTAATCTCA-ATAATTGTA
*
3260051 TATTATTTATTATCATTTATCTCAATAATT
1 TATT-TTTATTATCATTAATCTCAATAATT
3260081 TGATACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 4 0.15
33 13 0.50
34 9 0.35
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (32 bp):
TATTTTTATTATCATTAATCTCAATAATTGTA
Found at i:3267872 original size:37 final size:37
Alignment explanation
Indices: 3267762--3268154 Score: 273
Period size: 37 Copynumber: 11.0 Consensus size: 37
3267752 ATAGTATATT
*
3267762 TTTTTGAAAATATTTTTGAAAA-A-ATATAATATATAA
1 TTTTTGAAAACATTTTT-AAAATATATATAATATATAA
* * * *
3267798 TTTTCAGGAAACAGTTTTCCAAAATATATATATTATATAA
1 TTTT-TGAAAACA-TTTT-TAAAATATATATAATATATAA
3267838 TTTTTGAAAACATTTTTAAAATATATATAATATAT-A
1 TTTTTGAAAACATTTTTAAAATATATATAATATATAA
*
3267874 GTTTTGAAAACA--TTT---ATATAT-T-ATATAGT--
1 TTTTTGAAAACATTTTTAAAATATATATAATATA-TAA
***
3267903 TTTAAAAAAACATTTTTAAAATATATATAATATAT-A
1 TTTTTGAAAACATTTTTAAAATATATATAATATATAA
*
3267939 GTTTTGAAAACA--TTT---ATATAT-T-ATATAGT--
1 TTTTTGAAAACATTTTTAAAATATATATAATATA-TAA
*** *
3267968 TTTAAAAAAACATTTTGAAAATATATATAATATA-AA
1 TTTTTGAAAACATTTTTAAAATATATATAATATATAA
*
3268004 GTTTTT-AAAACATTTTGAAAAATATATATAATATAT-A
1 -TTTTTGAAAACATTTT-TAAAATATATATAATATATAA
* * *
3268041 GTTTTAAAAACATTTTTGAAAATATATATAATATATAG
1 TTTTTGAAAACATTTTT-AAAATATATATAATATATAA
* *
3268079 TTTTT-AAAACATTTTTGAAAACTTATAAATAATATATAG
1 TTTTTGAAAACATTTTT-AAAA--TATATATAATATATAA
* *
3268118 TTTTT-AAACCATTTTTGAATATATATATATATATATA
1 TTTTTGAAAACATTTTT-AAAATATATATA-ATATATA
3268155 TATATATATT
Statistics
Matches: 290, Mismatches: 34, Indels: 64
0.75 0.09 0.16
Matches are distributed among these distances:
29 26 0.09
30 4 0.01
31 17 0.06
34 18 0.06
35 3 0.01
36 48 0.17
37 94 0.32
38 23 0.08
39 41 0.14
40 16 0.06
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAACATTTTTAAAATATATATAATATATAA
Found at i:3267883 original size:25 final size:25
Alignment explanation
Indices: 3267850--3267910 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 25
3267840 TTTGAAAACA
*
3267850 TTTTTAAAATATATATAATATATAG
1 TTTTAAAAATATATATAATATATAG
* *
3267875 TTTTGAAAACATTTATATATTATATAG
1 TTTT-AAAA-ATATATATAATATATAG
3267902 TTTTAAAAA
1 TTTTAAAAA
3267911 AACATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 5 0.16
26 7 0.23
27 19 0.61
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
TTTTAAAAATATATATAATATATAG
Found at i:3267899 original size:27 final size:27
Alignment explanation
Indices: 3267861--3267975 Score: 104
Period size: 27 Copynumber: 3.9 Consensus size: 27
3267851 TTTTAAAATA
* *
3267861 TATATAATATATAGTTTTGAAAACATT
1 TATATATTATATAGTTTTAAAAACATT
3267888 TATATATTATATAGTTTTAAAAAAACATTTTT
1 TATATATTATATAGTTTT--AAAAACA---TT
*
3267920 AAAATATATATAATATATAGTTTTGAAAACATT
1 ----TATATAT--TATATAGTTTTAAAAACATT
3267953 TATATATTATATAGTTTTAAAAA
1 TATATATTATATAGTTTTAAAAA
3267976 AACATTTTGA
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
27 32 0.44
29 13 0.18
32 2 0.03
33 2 0.03
36 13 0.18
38 11 0.15
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (27 bp):
TATATATTATATAGTTTTAAAAACATT
Found at i:3267922 original size:65 final size:64
Alignment explanation
Indices: 3267824--3268092 Score: 351
Period size: 65 Copynumber: 4.0 Consensus size: 64
3267814 TTCCAAAATA
* **
3267824 TATATATTATATAATTTTTGAAAACATTTTTAAAATATATATAATATATAGTTTTGAAAACATT
1 TATATATTATATAGTTTTAAAAAACATTTTTAAAATATATATAATATATAGTTTTGAAAACATT
3267888 TATATATTATATAGTTTTAAAAAAACATTTTTAAAATATATATAATATATAGTTTTGAAAACATT
1 TATATATTATATAGTTTT-AAAAAACATTTTTAAAATATATATAATATATAGTTTTGAAAACATT
* * *
3267953 TATATATTATATAGTTTTAAAAAAACATTTTGAAAATATATATAATATAAAGTTTTTAAAACATT
1 TATATATTATATAGTTTT-AAAAAACATTTTTAAAATATATATAATATATAGTTTTGAAAACA--
3268018 TT
63 TT
*
3268020 GAAAAATATATATAATATATAGTTTT-AAAAACATTTTTGAAAATATATATAATATATAGTTTTT
1 ------TATATAT--TATATAGTTTTAAAAAACATTTTT-AAAATATATATAATATATAGTTTTG
3268084 AAAACATT
57 AAAACATT
3268092 T
1 T
3268093 TTGAAAACTT
Statistics
Matches: 185, Mismatches: 8, Indels: 22
0.86 0.04 0.10
Matches are distributed among these distances:
64 17 0.09
65 104 0.56
66 1 0.01
67 2 0.01
72 2 0.01
73 18 0.10
74 30 0.16
75 11 0.06
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (64 bp):
TATATATTATATAGTTTTAAAAAACATTTTTAAAATATATATAATATATAGTTTTGAAAACATT
Found at i:3267992 original size:29 final size:27
Alignment explanation
Indices: 3267926--3267994 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
3267916 TTTTAAAATA
* *
3267926 TATATAATATATAGTTTTGAAAACATT
1 TATAAAATATATAGTTTTAAAAACATT
* *
3267953 TATATATTATATAGTTTTAAAAAAACATT
1 TATAAAATATATAGTTTT--AAAAACATT
3267982 T-TGAAAATATATA
1 TAT-AAAATATATA
3267995 TAATATAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 17 0.49
28 1 0.03
29 17 0.49
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (27 bp):
TATAAAATATATAGTTTTAAAAACATT
Found at i:3268143 original size:2 final size:2
Alignment explanation
Indices: 3268136--3268163 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3268126 CCATTTTTGA
3268136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3268164 TAGTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3268193 original size:92 final size:88
Alignment explanation
Indices: 3268062--3268333 Score: 369
Period size: 90 Copynumber: 3.1 Consensus size: 88
3268052 ATTTTTGAAA
3268062 ATATATATA-ATATA-TAGTTTTT-AAAACATTTTTGAAAACTTATAAATAATATATAGTTTTTA
1 ATATATATATATATATTAGTTTTTAAAAACATTTTTGAAAACTTATAAATAATATATAGTTTTTA
*
3268124 AACCATTTTTGAATATATATATAT
66 AAACATTTTT-AATATATATATAT
3268148 ATATATATATATATATTAGTTTTTAAAAAACATTTTTTTGAAAACTTAT--ATAATATATAGTTT
1 ATATATATATATATATTAGTTTTT-AAAAACA--TTTTTGAAAACTTATAAATAATATATAGTTT
*
3268211 TTAAAATATTTTTAAATATATATATAT
63 TTAAAACATTTTT-AATATATATATAT
* * *
3268238 ATATATATATATATTATATAGGTTTTAAAAACATTTTTGAAAACTTA-AATATAATACATAATTT
1 ATATATATATATA-TAT-TAGTTTTTAAAAACATTTTTGAAAACTTATAA-ATAATATATAGTTT
*
3268302 TTAAAACATTTTTAAAATATATATAT
63 TTAAAACATTTTTAATATATATATAT
3268328 -TATATA
1 ATATATA
3268334 GGTTTTAAAA
Statistics
Matches: 167, Mismatches: 8, Indels: 19
0.86 0.04 0.10
Matches are distributed among these distances:
86 9 0.05
87 5 0.03
88 8 0.05
89 20 0.12
90 69 0.41
91 34 0.20
92 22 0.13
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (88 bp):
ATATATATATATATATTAGTTTTTAAAAACATTTTTGAAAACTTATAAATAATATATAGTTTTTA
AAACATTTTTAATATATATATAT
Found at i:3268233 original size:2 final size:2
Alignment explanation
Indices: 3268226--3268257 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3268216 ATATTTTTAA
3268226 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3268258 GGTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3268380 original size:26 final size:27
Alignment explanation
Indices: 3268350--3268401 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
3268340 AAAAATATTT
* *
3268350 TTTATTTATTATTA-TTATTATTGTTA
1 TTTATATATTAATATTTATTATTGTTA
*
3268376 TTTATATATTAATATTTATTTTTGTT
1 TTTATATATTAATATTTATTATTGTT
3268402 TTTTGTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTATATATTAATATTTATTATTGTTA
Found at i:3272717 original size:85 final size:85
Alignment explanation
Indices: 3272573--3273727 Score: 1286
Period size: 85 Copynumber: 13.6 Consensus size: 85
3272563 TTACAGCATA
* * * * *
3272573 GCGAGAAGGGTTATCTGTTAAAAAAGACCTTCGAGTTTGATTACATTCAGCTCAGAGGCAAATCA
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
*
3272638 AATTTACAGCATAGCTCAAG
66 AATTTACAGCATAACTCAAG
* *
3272658 GCGAGAATGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTATATTCAGCTCAAAGGCATATC-
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
* * *
3272722 TA-GTACAACATAACTCAAG
66 AATTTACAGCATAACTCAAG
* * * * * *
3272741 GCGAGAAGGGTTATCTGTCAACCAAGACCTTTGAGTTCGATTACACTCAG--C-AAGGAACATTA
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
* * * *
3272803 AATTTGCAACATAGCTTAAG
66 AATTTACAGCATAACTCAAG
** * * * * *
3272823 GCGAGAAGGACTATCTGTCAACAAAATACCTTCGAGTTTGATTACTTTTAGCTCAAAAGCATATC
1 GCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATC
* * *
3272888 -CA-GTACAACATAACTCAAG
65 AAATTTACAGCATAACTCAAG
* * * * * *
3272907 GTGAGAAAGGTTATTTGTCAGCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACATATCA
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
* * *
3272972 AATTTACAGCTTAGCTTAAG
66 AATTTACAGCATAACTCAAG
** * * * *
3272992 GCGAGAAGGGTTATCTGTCAGTAAAGACCTCCGAGTTTGATTACATTTAGCTCAAAAGCATATCA
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
*
3273057 AATTTACAACATAACTCAAG
66 AATTTACAGCATAACTCAAG
* * * *
3273077 GCAAGAAGGGTTATCTGTCAGGC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC
1 GCGAGAAGGGTTATCTGTCA-ACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATC
*
3273141 AAATCATACAGCATAACTCAAG
65 AAAT-TTACAGCATAACTCAAG
* * * *
3273163 GCGAGAAGGGTTATCTGTCAGCAAAGACTTTCGAGTTTGATTACACTCAGCTCAAAGGCATATCA
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
* *
3273228 AATTTACAGCATAGCTTAAG
66 AATTTACAGCATAACTCAAG
* * *
3273248 GCGAGAAGGGTCATCTGTCAACAAAGACTTTCAAGTTCGATTACATTCAGCTCAAAGGCATATCA
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
3273313 AATTTACAGCATAACTCAAG
66 AATTTACAGCATAACTCAAG
* * * * * *
3273333 GCGAGAAGGATTATCTTTCAGCCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATC-
3273398 AAATTTACAGCATAACTCAAG
65 AAATTTACAGCATAACTCAAG
* * * * *
3273419 GCGAGAATGGCTATTTGTCATCAAAGACCTTCGATTTCGATTACATTCAGCTCAAAGGCATATCA
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
*
3273484 AATTTATAGCATAACTCAAG
66 AATTTACAGCATAACTCAAG
* * * * * * *
3273504 GCAAGAAGGGTTATCTGTCAGCTAAGACCTTCGAGTTCGAATACACTCAGTTCAAAGGCACATCA
1 GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
* *
3273569 AATTTATAGCATAGCTCAAG
66 AATTTACAGCATAACTCAAG
* * * *
3273589 GCGAGAAGAGTTATCTGTCAATAAAAGACCTTCGAGTTTGATTACACTT-AGCTCAAAGGCACAT
1 GCGAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTACA-TTCAGCTCAAAGGCATAT
* ** * * *
3273653 CGAATACACAACATAGCTTAAG
64 CAAATTTACAGCATAACTCAAG
* * ** * * *
3273675 TCAAGAAAAGTTATCTTTCAACAAA-AACTGTCGAGTTCGATTCCATTCAGCTC
1 GCGAGAAGGGTTATCTGTCAACAAAGACCT-TCGAGTTCGATTACATTCAGCTC
3273728 GATGAAACAT
Statistics
Matches: 900, Mismatches: 154, Indels: 32
0.83 0.14 0.03
Matches are distributed among these distances:
80 7 0.01
81 2 0.00
82 33 0.04
83 115 0.13
84 36 0.04
85 481 0.53
86 225 0.25
87 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (85 bp):
GCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCA
AATTTACAGCATAACTCAAG
Found at i:3273207 original size:256 final size:255
Alignment explanation
Indices: 3272423--3273727 Score: 1474
Period size: 256 Copynumber: 5.2 Consensus size: 255
3272413 ATTCAAAAGC
* * *
3272423 ATCTGCCAACAAAGACCTTCGAGTTCGATCACACTCAGCTCAGAGGCATATCAAATTTACAGCAT
1 ATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* * * * *
3272488 AGCTCAAGGCGAGAAGGGCTATCTGTCAA-AAAGACCTTTGAGTTTGATTACATTTAGCTCAGAG
66 AGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAG
* * * *
3272552 GCAAATCAAATTTACAGC---A-T--A-GCGAGAAGGGTTATCTGTTAAAAAAGACCTTCGAGTT
131 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAGACAAGACCTTCGAGTT
* * * * *
3272610 TGATTACATTCAGCTCAGAGGCAAATCAAATTTACAGCATAGCTCAAGGCGAGAATGGTT
196 TGATTACACTCAGCTCAAAGGCACATCAAATATACAGCATAACTCAAGGCGAGAATGGTT
* * * * *
3272670 ATCTGTCAACAAAGACCTTCGAGTTCGATTATATTCAGCTCAAAGGCATATC-TA-GTACAACAT
1 ATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* * * *
3272733 AACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTTGAGTTCGATTACACTCAG--C-AAG
66 AGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAG
* * * * * * * ** *
3272795 GAACATTAAATTTGCAACATAGCTTAAGGCGAGAAGGACTATCTGTCA-ACAAAATACCTTCGAG
131 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAGAC--AAGACCTTCGAG
** * * * * * * * *
3272859 TTTGATTACTTTTAGCTCAAAAGCATATC-CA-GTACAACATAACTCAAGGTGAGAAAGGTT
194 TTTGATTACACTCAGCTCAAAGGCACATCAAATATACAGCATAACTCAAGGCGAGAATGGTT
* * * *
3272919 ATTTGTCAGCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACATATCAAATTTACAGCTT
1 ATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* ** * * * *
3272984 AGCTTAAGGCGAGAAGGGTTATCTGTCAGTAAAGACCTCCGAGTTTGATTACATTTAGCTCAAAA
66 AGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAG
* * *
3273049 GCATATCAAATTTACAACATAACTCAAGGCAAGAAGGGTTATCTGTCAGGCAAGACCTTCGAGTT
131 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAGACAAGACCTTCGAGTT
* *
3273114 CGATTACACTCAGCTCAAAGGCACATCAAATCATACAGCATAACTCAAGGCGAGAAGGGTT
196 TGATTACACTCAGCTCAAAGGCACATCAAAT-ATACAGCATAACTCAAGGCGAGAATGGTT
* * *
3273175 ATCTGTCAGCAAAGACTTTCGAGTTTGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
1 ATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* * * *
3273240 AGCTTAAGGCGAGAAGGGTCATCTGTCAACAAAGACTTTCAAGTTCGATTACATTCAGCTCAAAG
66 AGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAG
* * *
3273305 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGATTATCTTTCAGCCAAGACCTTCGAGTT
131 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAGACAAGACCTTCGAGTT
* * *
3273370 CGATTACACTCAGCTCAAAGGCACATCAAAATTTACAGCATAACTCAAGGCGAGAATGGCT
196 TGATTACACTCAGCTCAAAGGCACATC-AAATATACAGCATAACTCAAGGCGAGAATGGTT
* * * * *
3273431 ATTTGTCATCAAAGACCTTCGATTTCGATTACATTCAGCTCAAAGGCATATCAAATTTATAGCAT
1 ATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* * * * * * *
3273496 AACTCAAGGCAAGAAGGGTTATCTGTCAGCTAAGACCTTCGAGTTCGAATACACTCAGTTCAAAG
66 AGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAG
* * * * * *
3273561 GCACATCAAATTTATAGCATAGCTCAAGGCGAGAAGAGTTATCTGTCAATAAAAGACCTTCGAGT
131 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-AGACAAGACCTTCGAGT
* * * * * * * * **
3273626 TTGATTACACTTAGCTCAAAGGCACATCGAATACACAACATAGCTTAAGTCAAGAAAAGTT
195 TTGATTACACTCAGCTCAAAGGCACATCAAATATACAGCATAACTCAAGGCGAGAATGGTT
* * * *
3273687 ATCTTTCAACAAA-AACTGTCGAGTTCGATTCCATTCAGCTC
1 ATCTGTCAACAAAGACCT-TCGAGTTCGATTACACTCAGCTC
3273728 GATGAAACAT
Statistics
Matches: 889, Mismatches: 147, Indels: 35
0.83 0.14 0.03
Matches are distributed among these distances:
243 15 0.02
244 1 0.00
245 34 0.04
246 25 0.03
247 48 0.05
249 73 0.08
250 19 0.02
251 89 0.10
253 35 0.04
254 42 0.05
255 4 0.00
256 460 0.52
257 44 0.05
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (255 bp):
ATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
AGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAG
GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAGACAAGACCTTCGAGTT
TGATTACACTCAGCTCAAAGGCACATCAAATATACAGCATAACTCAAGGCGAGAATGGTT
Found at i:3273231 original size:171 final size:169
Alignment explanation
Indices: 3272423--3273727 Score: 1418
Period size: 171 Copynumber: 7.7 Consensus size: 169
3272413 ATTCAAAAGC
* * *
3272423 ATCTGCCAACAAAGACCTTCGAGTTCGATCACACTCAGCTCAGAGGCATATCAAATTTACAGCAT
1 ATCTGTCAAC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* * * * *
3272488 AGCTCAAGGCGAGAAGGGCTATCTGTCA-AAAAGACCTTTGAGTTTGATTACATTTAGCTCAGAG
65 AGCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAG
*
3272552 GCAAATCAAATTTACAGC---A-T--A-GCGAGAAGGGTT
130 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTT
* * * * * *
3272585 ATCTGTTAAAAAAGACCTTCGAGTTTGATTACATTCAGCTCAGAGGCAAATCAAATTTACAGCAT
1 ATCTG-TCAACAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* * * *
3272650 AGCTCAAGGCGAGAATGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTATATTCAGCTCAAAG
65 AGCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAG
* * *
3272715 GCATATC-TA-GTACAACATAACTCAAGGCGAGAAGGGTT
130 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTT
* * * * * *
3272753 ATCTGTCAACCAAGACCTTTGAGTTCGATTACACTCAG--C-AAGGAACATTAAATTTGCAACAT
1 ATCTGTCAA-CAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* ** * * * *
3272815 AGCTTAAGGCGAGAAGGACTATCTGTCAACAAAATACCTTCGAGTTTGATTACTTTTAGCTCAAA
65 AGCTCAAGGCGAGAAGGGTTATCTGTCAGC-AAAGACCTTCGAGTTTGATTACATTCAGCTCAAA
* * * * * *
3272880 AGCATATC-CA-GTACAACATAACTCAAGGTGAGAAAGGTT
129 GGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTT
* * * *
3272919 ATTTGTCAGCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACATATCAAATTTACAGCTT
1 ATCTGTCAAC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* * * * *
3272984 AGCTTAAGGCGAGAAGGGTTATCTGTCAGTAAAGACCTCCGAGTTTGATTACATTTAGCTCAAAA
65 AGCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAG
* *
3273049 GCATATCAAATTTACAACATAACTCAAGGCAAGAAGGGTT
130 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTT
* * *
3273089 ATCTGTCAGGCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATCATACAGCA
1 ATCTGTCA-ACAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAAT-TTACAGCA
* * *
3273154 TAACTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACTTTCGAGTTTGATTACACTCAGCTCAAA
64 TAGCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTTGATTACATTCAGCTCAAA
* * *
3273219 GGCATATCAAATTTACAGCATAGCTTAAGGCGAGAAGGGTC
129 GGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTT
* * *
3273260 ATCTGTCAACAAAGACTTTCAAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAGCAT
1 ATCTGTCAAC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* * * * * *
3273325 AACTCAAGGCGAGAAGGATTATCTTTCAGCCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAG
65 AGCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAG
* * *
3273390 GCACATCAAAATTTACAGCATAACTCAAGGCGAGAATGGCT
130 GCATATC-AAATTTACAGCATAACTCAAGGCGAGAAGGGTT
* * * * *
3273431 ATTTGTCATCAAAGACCTTCGATTTCGATTACATTCAGCTCAAAGGCATATCAAATTTATAGCAT
1 ATCTGTCAAC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCAT
* * * * * * *
3273496 AACTCAAGGCAAGAAGGGTTATCTGTCAGCTAAGACCTTCGAGTTCGAATACACTCAGTTCAAAG
65 AGCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAG
* * * *
3273561 GCACATCAAATTTATAGCATAGCTCAAGGCGAGAAGAGTT
130 GCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTT
* * * * * ** *
3273601 ATCTGTCAATAAAAGACCTTCGAGTTTGATTACACTTAGCTCAAAGGCACATCGAATACACAACA
1 ATCTGTC-A-ACAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCA
* * * ** * * * * *
3273666 TAGCTTAAGTCAAGAAAAGTTATCTTTCAACAAA-AACTGTCGAGTTCGATTCCATTCAGCTC
64 TAGCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCT-TCGAGTTTGATTACATTCAGCTC
3273728 GATGAAACAT
Statistics
Matches: 976, Mismatches: 143, Indels: 39
0.84 0.12 0.03
Matches are distributed among these distances:
161 5 0.01
162 82 0.08
163 38 0.04
164 1 0.00
165 45 0.05
166 98 0.10
167 4 0.00
168 81 0.08
169 43 0.04
170 187 0.19
171 392 0.40
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (169 bp):
ATCTGTCAACAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATA
GCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGG
CATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGTT
Found at i:3274401 original size:38 final size:38
Alignment explanation
Indices: 3274265--3274744 Score: 461
Period size: 38 Copynumber: 12.6 Consensus size: 38
3274255 TTGAAAATGT
* **
3274265 TTTTGAAAA-A-ATATA-ATATATAATTTTCAGAAAACGA
1 TTTTGAAAACATATATATATATATAGTTTT-TTAAAAC-A
* *
3274302 TTTTCAAAATATATATAT-TATATAGTTTTTTAAAACA
1 TTTTGAAAACATATATATATATATAGTTTTTTAAAACA
* * *
3274339 TTTTTAAAATATATATA-ATATATAG-TTTTGAAAACA
1 TTTTGAAAACATATATATATATATAGTTTTTTAAAACA
* *
3274375 TTTTGAAAACATTTATATATCATATAGTTTTTAAAAAACA
1 TTTTGAAAACATATATATAT-ATATAGTTTTT-TAAAACA
*
3274415 TTTTGAAAATATATATAT-TATATAGTTTTTTAAAACA
1 TTTTGAAAACATATATATATATATAGTTTTTTAAAACA
*
3274452 TTTTGAAAATATATATATAATATATAG-TTTTTAAAACA
1 TTTTGAAAACATATATAT-ATATATAGTTTTTTAAAACA
*
3274490 -TTTGAAAATATATATA-ATATATAGTTTTTTAAAACA
1 TTTTGAAAACATATATATATATATAGTTTTTTAAAACA
** *
3274526 TTTTTTTAAACTTATATATAATATATAG--TTTTAAAACA
1 -TTTTGAAAACATATATAT-ATATATAGTTTTTTAAAACA
* *
3274564 TTTTTGAAAATATATATAT-TATATAGTTTTTAAAAAAACA
1 -TTTTGAAAACATATATATATATATAGTTTTT--TAAAACA
*
3274604 TTTTTTTGAAAACTTATATA-ATATATAG-TTTTTAAAACA
1 ---TTTTGAAAACATATATATATATATAGTTTTTTAAAACA
* *
3274643 TTTTTGAAAAAAATATATATAGTATATAGTTTTTAAAAACA
1 -TTTTG-AAAACATATATATA-TATATAGTTTTTTAAAACA
* *
3274684 TTTTTGAAAACTTAAATATAATATATAG-TTTTTAAAACA
1 -TTTTGAAAACATATATAT-ATATATAGTTTTTTAAAACA
* *
3274723 TTTTTAAAATATATATATATAT
1 TTTTGAAAACATATATATATAT
3274745 TATATAGTGT
Statistics
Matches: 380, Mismatches: 36, Indels: 54
0.81 0.08 0.11
Matches are distributed among these distances:
35 8 0.02
36 42 0.11
37 84 0.22
38 98 0.26
39 44 0.12
40 60 0.16
41 21 0.06
42 23 0.06
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
TTTTGAAAACATATATATATATATAGTTTTTTAAAACA
Found at i:3274767 original size:40 final size:38
Alignment explanation
Indices: 3274239--3274767 Score: 472
Period size: 37 Copynumber: 13.7 Consensus size: 38
3274229 ATATATAGTA
* **
3274239 ATATAGTATATTGTTTTTGAAAATGTTTTTGAAAAA-ATAT
1 ATATA-TATATAGTTTTT-AAAACATTTTT-AAAAATATAT
* *
3274279 A-ATATATA-A-TTTTCAGAAAACGA-TTTTCAAAATATAT
1 ATATATATATAGTTTT--TAAAAC-ATTTTTAAAAATATAT
3274316 ATAT-TATATAGTTTTTTAAAACATTTTT-AAAATATAT
1 ATATATATATAG-TTTTTAAAACATTTTTAAAAATATAT
* *
3274353 ATA-ATATATAGTTTTGAAAACATTTTGAAAACAT-T-T
1 ATATATATATAGTTTTTAAAACATTTTTAAAA-ATATAT
*
3274389 ATATATCATATAGTTTTTAAAAAACA-TTTTGAAAATATAT
1 ATATAT-ATATAGTTTTT--AAAACATTTTTAAAAATATAT
*
3274429 ATAT-TATATAGTTTTTTAAAACA-TTTTGAAAATATAT
1 ATATATATATAG-TTTTTAAAACATTTTTAAAAATATAT
*
3274466 ATATAATATATAGTTTTTAAAACA--TTTGAAAATATAT
1 ATAT-ATATATAGTTTTTAAAACATTTTTAAAAATATAT
* *
3274503 ATA-ATATATAGTTTTTTAAAACATTTTTTTAAACT-TAT
1 ATATATATATAG-TTTTTAAAACA-TTTTTAAAAATATAT
*
3274541 ATATAATATATAG-TTTTAAAACATTTTTGAAAATATAT
1 ATAT-ATATATAGTTTTTAAAACATTTTTAAAAATATAT
*
3274579 ATAT-TATATAGTTTTTAAAAAAACATTTTTTTGAAAACT-TAT
1 ATATATATATAGTTTTT---AAAACA--TTTTT-AAAAATATAT
*
3274621 ATA-ATATATAGTTTTTAAAACATTTTTGAAAAAAATAT
1 ATATATATATAGTTTTTAAAACATTTTT-AAAAATATAT
* *
3274659 ATATAGTATATAGTTTTTAAAAACATTTTTGAAAACT-TAA
1 ATATA-TATATAGTTTTT-AAAACATTTTT-AAAAATATAT
3274699 ATATAATATATAGTTTTTAAAACATTTTTAAAATATATAT
1 ATAT-ATATATAGTTTTTAAAACATTTTTAAAA-ATATAT
* *
3274739 ATATATTATATAGTGTTTAAAATATTTTT
1 ATATA-TATATAGTTTTTAAAACATTTTT
3274768 TATTTATTTG
Statistics
Matches: 419, Mismatches: 26, Indels: 88
0.79 0.05 0.17
Matches are distributed among these distances:
35 8 0.02
36 44 0.11
37 106 0.25
38 80 0.19
39 50 0.12
40 87 0.21
41 17 0.04
42 23 0.05
43 4 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (38 bp):
ATATATATATAGTTTTTAAAACATTTTTAAAAATATAT
Found at i:3275952 original size:17 final size:17
Alignment explanation
Indices: 3275930--3275967 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3275920 TCCTTTACAC
*
3275930 TTTTATTTAT-TTATTTA
1 TTTTATATATATT-TTTA
3275947 TTTTATATATATTTTTA
1 TTTTATATATATTTTTA
3275964 TTTT
1 TTTT
3275968 CTCTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATATATATTTTTA
Found at i:3276811 original size:27 final size:27
Alignment explanation
Indices: 3276781--3276846 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
3276771 TGACCCGTTC
3276781 ATATTTTTATTTTTTAAAATATTTATG
1 ATATTTTTATTTTTTAAAATATTTATG
3276808 ATATTTTTATTTTTTAAAATATTTATG
1 ATATTTTTATTTTTTAAAATATTTATG
*
3276835 ATATTTTAATTT
1 ATATTTTTATTT
3276847 AACATTTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (27 bp):
ATATTTTTATTTTTTAAAATATTTATG
Found at i:3277933 original size:10 final size:10
Alignment explanation
Indices: 3277918--3277943 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3277908 TGGTTGGGAA
3277918 CCAGCCTCCT
1 CCAGCCTCCT
3277928 CCAGCCTCCT
1 CCAGCCTCCT
3277938 CCAGCC
1 CCAGCC
3277944 GACGGTGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.62, G:0.12, T:0.15
Consensus pattern (10 bp):
CCAGCCTCCT
Found at i:3278506 original size:22 final size:22
Alignment explanation
Indices: 3278475--3278516 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3278465 CCGTTAACCA
*
3278475 TTGACATGTCTGACCGTTGATT
1 TTGACATGTCAGACCGTTGATT
*
3278497 TTGACTTGTCAGACCGTTGA
1 TTGACATGTCAGACCGTTGA
3278517 CCGTTGCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (22 bp):
TTGACATGTCAGACCGTTGATT
Found at i:3278559 original size:18 final size:18
Alignment explanation
Indices: 3278536--3278571 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3278526 TTGAGTTTGA
3278536 CTGAAAAAGTCAA-ATTTT
1 CTGAAAAAG-CAATATTTT
3278554 CTGAAAAAGCAATATTTT
1 CTGAAAAAGCAATATTTT
3278572 ATATTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
CTGAAAAAGCAATATTTT
Found at i:3280458 original size:31 final size:30
Alignment explanation
Indices: 3280420--3280524 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 30
3280410 AGACTCTGGC
3280420 AGGTTCAGTCGTTGCTGGTAATTCCTTGTAT
1 AGGTTCAGTCG-TGCTGGTAATTCCTTGTAT
* * *
3280451 AGGTTCAGTACCG-ACTGGTAATTCCTTATCTCT
1 AGGTTCAGT--CGTGCTGGTAATTCC-T-TGTAT
*
3280484 GGCAGGTTCAGTCGCTGTTGGTAATTCCTTGTAT
1 ---AGGTTCAGTCG-TGCTGGTAATTCCTTGTAT
3280518 AGGTTCA
1 AGGTTCA
3280525 ACACAGATTG
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
31 27 0.47
32 1 0.02
33 5 0.09
34 5 0.09
35 1 0.02
36 19 0.33
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (30 bp):
AGGTTCAGTCGTGCTGGTAATTCCTTGTAT
Found at i:3280521 original size:67 final size:67
Alignment explanation
Indices: 3280413--3280546 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 67
3280403 TGACTGAAGA
* ** *
3280413 CTCTGGCAGGTTCAGTCGTTGCTGGTAATTCCTTGTATAGGTTCAGTACCGACTGGTAATTCCTT
1 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTTGTATAGGTTCAACACAGACTGGTAATTCCTT
3280478 AT
66 AT
* *
3280480 CTCTGGCAGGTTCAGTCGCTGTTGGTAATTCCTTGTATAGGTTCAACACAGATTGGTAATTCCTT
1 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTTGTATAGGTTCAACACAGACTGGTAATTCCTT
3280545 AT
66 AT
3280547 AGACCTAAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (67 bp):
CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTTGTATAGGTTCAACACAGACTGGTAATTCCTT
AT
Found at i:3281717 original size:18 final size:18
Alignment explanation
Indices: 3281694--3281742 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3281684 TTATTATAAA
3281694 ATATATTTTA-TTCTAATT
1 ATATATTTTATTTC-AATT
*
3281712 ATATATTTTTATTTCATTT
1 ATATA-TTTTATTTCAATT
*
3281731 TTATATTTTATT
1 ATATATTTTATT
3281743 ATAGATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.44
19 12 0.44
20 3 0.11
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATATTTTATTTCAATT
Done.